Contacts of the helix formed by residues 260 - 268 (chain C) in PDB entry 2W3S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 260 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C TYR* 4.4 2.0 - - - -
255C PHE* 4.8 6.7 - + - -
256C ALA* 2.9 20.8 + - + +
259C PRO* 1.3 111.2 + - + +
261C PRO* 1.3 68.4 - - - +
262C ALA* 3.1 4.0 - - - +
263C LEU* 2.9 25.6 + - + +
264C ALA 3.0 7.8 + - - -
301C MET* 3.5 29.2 - - + +
341C LEU* 4.1 22.1 - - + +
342C PRO* 3.2 28.1 + - + -
344C SER* 4.0 16.2 - - - -
345C ALA* 4.1 11.5 + - + +
348C LEU* 5.4 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ALA 3.3 5.4 - - - +
257C GLU* 4.3 9.9 - - + +
258C GLY 3.4 15.9 - - - +
259C PRO 3.6 2.9 - - - +
260C HIS* 1.3 87.4 - - - +
262C ALA* 1.3 57.3 + - - +
264C ALA* 3.3 5.8 + - + +
265C GLY* 2.8 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C HIS 3.1 1.4 - - - -
261C PRO* 1.3 79.3 - - - +
263C LEU* 1.3 61.7 + - - +
265C GLY* 3.4 1.4 + - - -
266C LEU* 3.0 23.6 + - - +
348C LEU* 3.4 43.3 - - + +
349C ARG* 4.3 11.7 - - - -
350C CYS* 3.9 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 4.3 18.6 - - + -
256C ALA* 4.0 16.6 - - + -
260C HIS* 2.9 18.7 + - + +
262C ALA* 1.3 78.0 - - - +
264C ALA* 1.3 56.6 + - - +
266C LEU* 3.2 9.1 + - + +
267C LEU* 2.9 45.1 + - + +
294C GLY* 5.3 2.7 - - - +
297C ALA* 3.8 27.8 - - + -
298C LEU* 4.3 14.6 - - + -
301C MET* 3.9 20.0 - - + -
341C LEU* 4.3 17.5 - - + -
348C LEU* 4.3 3.8 - - + +
350C CYS* 4.7 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ARG* 3.4 44.2 + - + +
256C ALA* 3.7 8.9 - - + +
257C GLU* 3.7 33.2 - - + +
260C HIS 3.0 5.3 + - - -
261C PRO* 3.8 6.5 - - + +
263C LEU* 1.3 76.6 - - - +
265C GLY* 1.3 61.1 + - - +
267C LEU* 4.6 1.1 - - - -
268C ARG* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ARG* 6.1 0.2 - - - -
261C PRO 2.8 17.2 + - - -
262C ALA 3.8 1.6 - - - -
264C ALA* 1.3 76.5 - - - +
266C LEU* 1.3 62.2 + - - +
268C ARG* 3.6 21.1 + - - +
269C ARG* 4.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ALA 3.0 14.0 + - - +
263C LEU* 3.4 11.9 - - + +
265C GLY* 1.3 76.0 - - - +
267C LEU* 1.3 61.3 + - + +
269C ARG* 3.0 25.3 + - - +
270C PHE* 3.7 3.6 + - - +
293C ASP* 3.5 34.7 - - + +
297C ALA* 3.5 23.6 - - + -
350C CYS* 3.8 26.4 + - + +
352C LYS* 3.9 34.1 - - + +
365C CYS* 4.3 12.6 - - - -
367C CYS* 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 3.7 24.9 - - + +
252C LEU* 3.8 34.5 - - + -
253C ARG* 3.8 25.1 - - + +
263C LEU* 2.9 36.9 + - + +
265C GLY 3.4 0.2 - - - -
266C LEU* 1.3 80.9 - - + +
268C ARG* 1.3 64.8 + - - +
269C ARG 3.0 2.2 - - - -
270C PHE* 3.0 43.5 + - + +
276C ARG* 3.2 15.8 + - - -
281C ILE* 6.2 0.7 - - + -
294C GLY* 5.4 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASP* 6.0 1.4 - - - +
127C ASP* 2.8 47.0 + - - +
253C ARG* 3.3 40.1 - - - +
264C ALA 3.2 7.8 + - - +
265C GLY* 3.6 15.6 + - - +
266C LEU 3.2 0.2 - - - -
267C LEU* 1.3 76.6 - - - +
269C ARG* 1.3 75.8 + - - +
271C ALA 4.6 0.5 - - - +
276C ARG* 3.1 24.5 + - - +
358C ASP* 4.1 18.7 + - - -
458C LEU* 3.7 29.3 - - - +
641D ARG* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il